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BEAST

BEAST

Description

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.


Available

Version on CSC's Servers


Taito: 1.7.5, 1.8.0, 1.10.1, 2.0.2, 2.1.2, 2.1.3, 2.4.3, 2.4.7, 2.5.1, 2.5.2


Usage

To load the default version on Taito you can use

module load biokit

or:

module load beast

To load a specific version you can use the version number, e.g.:

module load beast/2.1.3

To check the available versions use:

module spider beast

BEAST can be used either interactively with a graphical user interface or in command line mode. Any batch jobs need to be run in the command line mode. Interactive use is best done in Taito-shell. Longer runs should be done as batch jobs in Taito. You can of course use the graphical tools in Taito-shell to set up the run and the do the run itself in Taito.

To run with the GUI (you will need X server connection):

beauti

beast

To run in command line mode:

beast <options> example.xml

Sometimes you may need to give some extra options to Java, e.g. to increase MaxHeapSize. In these cases use:

java <java options> -jar $CLASSPATH/beast.jar

For example:

java -Xmx4g -jar $CLASSPATH/beast.jar example.xml

BEAST installation also includes helper programs FigTree and Tracer. They are set up when the BEAST module is loaded and are started with commands figtree and tracer respectively. Due to their interactive nature they are best used in Taito-shell.

You need a X server connection to use the graphical interfaces. If you have trouble setting this up, you might also consider running beauti locally on your own computer and transferring the resulting .xml files to CSC for analysis in command line mode.

BEAGLE

BEAGLE is a high-performance library that can improve the performance of BEAST. Depending on the dataset and analysis you can typically expect a 2x-3x speedup. To use BEAGLE you need to specify the appropriate options on the beast command line. You can try beagle_SSE and beagle_CPU options.

beast -beagle_SSE example.xml

beast -beagle_CPU example.xml

BEAGLE extensions are available on all servers.

BEAST 2 Packages

In BEAST 2.x many models and analysis methods are implemented as BEAST 2 Packages. For version management reasons these are not installed in the common installation, but they can be easily installed by each user as necessary.

You can use the either use the beauti interface (from the top menu select "File" -> "Manage packages") or use the command line addonmanager program.

To list available packages:

addonmanager -list

To install a package:

addonmanager -add SNAPP

To uninstall a package:

addonmanager -del SNAPP

 

Batch jobs in Taito

To submit a BEAST job in Taito, you must construct a xml file (see BEAST documentation for details) and a batch job script.

BEAST can use thread based parallelization that can speed up some analyses. In this example batch job script we run BEAST using 8 computing cores.

!/bin/bash -l

## name of your job
#SBATCH -J beast_example

## system error message output file
#SBATCH -e beast_example_err_%j

## system message output file
#SBATCH -o beast_example_output_%j

## a per-process (soft) memory limit
## limit is specified in MB
## example: 1 GB is 1000
#SBATCH --mem=8000

## how long a job takes, wallclock time hh:mm:ss
#SBATCH -t 01:00:00

## number of cores to use
#SBATCH -n 1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=8

## run my executable
beast -overwrite -seed 345 -beagle_sse -threads $SLURM_CPUS_PER_TASK benchmark1.xml > example.out

The batch job is submitted with command (where "my_job_script" is the name of your batch file):

sbatch my_job_script


Discipline

Biosciences

References


Support

servicedesk@csc.fi


Manual

For more information see the software home page: